Up to 50 passengers heading to Sri Lanka on a UK Border Agency forced-removals flight risk being tortured on their return, human rights organisations have warned.

The flight, which will depart on Thursday afternoon from an as yet undisclosed British airport, is expected to go ahead despite new evidence of recent alleged mistreatment by Sri Lankan security services.

The UK Border Agency has carried out two large-scale deportations to Sri Lanka since June, the last of which left from Luton airport in September, despite the concerns of several rights groups – including Amnesty International and Human Rights Watch – who believe that deported Tamils may be at risk of arbitrary arrest and mistreatment.

One London-based NGO, Freedom From Torture, which provides medical services to torture victims, has said that it has gathered evidence that demonstrates that prisoners in Sri Lanka were still facing severe mistreatment this year, more than two years after the island's 26-year civil war came to an end.

Last month, the United Nations' Committee Against Torture reported that it was "seriously concerned about the continued and consistent allegations of widespread use of torture and other cruel, inhuman or degrading treatment", after hearing submissions from a number of NGOs and the Sri Lankan government. The committee also expressed concern at "the prevailing climate of impunity" in Sri Lanka.

In a case recently referred to in a Border Agency report, Freedom from Torture documented that in spring this year a Sri Lankan national known as Rohan had been tortured after travelling back from the UK.

According to Freedom from Torture, Rohan, who held a UK student visa, claimed that after returning to visit a sick relative he was held by officials at Colombo airport and detained for three days where he was beaten stripped and his skin burned with heated metal.

At the airport the 32-year-old male was approached by two people claiming to be from Sri Lanka's Criminal Investigation Department who then bundled him into a van where he was tied up, blindfolded and beaten. He was subsequently taken to an undisclosed location where he was interrogated under duress about possible links to the Tamil Tigers (LTTE).

In a statement to Freedom from Torture Rohan said, "I was beaten up; I was burned with heated metal sticks. They removed my clothes and beat me with metal and wooden sticks. It was very painful. Afterwards I had blisters on my body and my face, hands and legs were swollen."

On the strength of his evidence of torture he was later granted asylum in the UK.

In an attempt to halt the flight, activist group Tamils Against Genocide has this week lodged a petition in the High Court claiming the UK government has failed in its obligation to review its deportations policy in light of new torture allegations.

The Guardian has also seen medical reports confirming that one of the passengers has TB, raising concerns that other passengers may be infected during the long haul flight.

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The UK Border Agency has warned officials who are deciding on asylum claims that the NGOs have serious concerns about forcibly returned Tamils. However, the agency is also circulating a report which quotes senior Sri Lankan intelligence officials as saying Tamil detainees are inflicting wounds upon themselves in order to create scars that will support later asylum claims.

The Border Agency says it only deports individuals "when we are satisfied the individual has no international protection needs", and cites a ruling by the European Court of Human Rights that not all Tamil asylum seekers are in need of protection.

Shortly before the last mass deportation flight in September, the Home Office claimed to be monitoring the welfare of people forcibly removed to Sri Lanka, and then conceded that it was not.

The Sri Lankan government describes allegations of ongoing torture as "unsubstantiated" and has said that media reports about the human rights groups' concerns are "malicious".

Freedom from Torture chief executive Keith Best said: "The UK Border Agency's recent bulletin updating country information for asylum decision-makers … is a really important step.

"Despite this evidence, which points to an ongoing risk of torture including to individuals with an actual or perceived association with the LTTE, the government is set to return another plane-load of Sri Lankans including refused asylum seekers without sufficient monitoring on return."